A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels andk-Mer Distances
نویسندگان
چکیده
منابع مشابه
A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k-Mer Distances
Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances, and to provide a lower misclassification rate when used with Support Vector Machines (SVMs). We confirm by independent experiments these two results, and propose in this article to use a coverage criterion to measure the seed efficiency in both cases in o...
متن کاملA coverage criterion for spaced seeds and its applications to SVM string-kernels and k-mer distances
Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (Onodera and Shibuya, 2013), We confirm by independent experiments these two results, and propo...
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We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize these regions that allow marked improvements in both specificity and sensitivity over existing techniques for sequence alignment. For any such characterization, which we call a vector seed, we give...
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We propose a method for support vector machine classification using indefinite kernels. Instead of directly minimizing or stabilizing a nonconvex loss function, our algorithm simultaneously computes support vectors and a proxy kernel matrix used in forming the loss. This can be interpreted as a penalized kernel learning problem where indefinite kernel matrices are treated as a noisy observation...
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MOTIVATION Metagenomics is a powerful approach to study genetic content of environmental samples, which has been strongly promoted by next-generation sequencing technologies. To cope with massive data involved in modern metagenomic projects, recent tools rely on the analysis of k-mers shared between the read to be classified and sampled reference genomes. RESULTS Within this general framework...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2014
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2014.0173